Re: AMBER: xleap screen output

From: Francesco Pietra <>
Date: Tue, 4 Mar 2008 09:27:00 -0800 (PST)

I could reproduce the xleap preparation of prmtop/inpcrd files with the my
previous membrane/protein/ligand system.

Though this new system only differs in the ligand, it required a whole setup
and I am still in open waters. I repeated the whole procedure (starting from
the same best pose from DOCK) and the pdb layouts match those successful above.

>From the warning messages while creating models in xleap the problems seem to
be with the membrane: xleap added 152 missing atoms. Curiously, it insists
that, e.g. SH11 and RH11 do not have a type (atoms of the lipid), while in the
pdb file these are correctly (correctly for leap) H11S and H11R. I.e., it says
atom names are wrong, though they are right and correctly positioned in the
file (13-16 columns) while single-letter atom names are at column 14. No
warning message with the protein complex pdb.

Probably the best would be to drop the matter for a week. until prejudices are
over. At any event, as I could reproduce the former process, no bug in the
program can be claimed.


--- Bill Ross <> wrote:

> > FATAL: Atom .R<E 2700>.A<H 1> does not have a type.
> A residue name of 'E' sounds suspicious - if your residue names
> don't include 'E' I would suspect the pdb file is malformed with
> the residue name wrongly positioned. Since the error msg continues
> with gibberish, it may be worthwhile for a developer to probe why
> this is so, but in the short run you should double-check your pdb
> format.
> Bill
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Received on Wed Mar 05 2008 - 06:07:34 PST
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